I personally wouldnt. Autos are much more sensitive to overfeeding. If I were you, I would pick up some rapid rooter cubes and as soon as your autos break the surface, transplant them into their final pot. The idea is to do this before the root leaves the cube. This way it's a transplant that the plant doesnt actually feel.
Just seems like an easier and safer way. Rapid rooter cubes are cheap too. I don't even use the paper towel method anymore, I just drop the seed right in and have had 100% germination so far.